# | Line 1 | Line 1 | |
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1 | < | /* |
1 | > | /* |
2 | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. | |
3 | * | |
4 | * The University of Notre Dame grants you ("Licensee") a | |
# | Line 47 | Line 47 | |
47 | * @version 1.0 | |
48 | */ | |
49 | ||
50 | – | #include <sprng.h> |
51 | – | |
50 | #include "brains/MoleculeCreator.hpp" | |
51 | #include "brains/SimCreator.hpp" | |
52 | #include "brains/SimSnapshotManager.hpp" | |
# | Line 57 | Line 55 | |
55 | #include "UseTheForce/ForceFieldFactory.hpp" | |
56 | #include "utils/simError.h" | |
57 | #include "utils/StringUtils.hpp" | |
58 | + | #include "math/SeqRandNumGen.hpp" |
59 | #ifdef IS_MPI | |
60 | #include "io/mpiBASS.h" | |
61 | < | #include "math/randomSPRNG.hpp" |
61 | > | #include "math/ParallelRandNumGen.hpp" |
62 | #endif | |
63 | ||
64 | namespace oopse { | |
65 | < | |
66 | < | void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
67 | < | |
65 | > | |
66 | > | void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, |
67 | > | Globals* simParams){ |
68 | > | |
69 | #ifdef IS_MPI | |
70 | < | |
70 | > | |
71 | if (worldRank == 0) { | |
72 | #endif // is_mpi | |
73 | < | |
74 | < | simParams->initalize(); |
75 | < | set_interface_stamps(stamps, simParams); |
76 | < | |
73 | > | |
74 | > | simParams->initalize(); |
75 | > | set_interface_stamps(stamps, simParams); |
76 | > | |
77 | #ifdef IS_MPI | |
78 | < | |
79 | < | mpiEventInit(); |
80 | < | |
78 | > | |
79 | > | mpiEventInit(); |
80 | > | |
81 | #endif | |
82 | < | |
83 | < | yacc_BASS(mdFileName.c_str()); |
84 | < | |
82 | > | |
83 | > | yacc_BASS(mdFileName.c_str()); |
84 | > | |
85 | #ifdef IS_MPI | |
86 | < | |
87 | < | throwMPIEvent(NULL); |
86 | > | |
87 | > | throwMPIEvent(NULL); |
88 | } else { | |
89 | < | set_interface_stamps(stamps, simParams); |
90 | < | mpiEventInit(); |
91 | < | MPIcheckPoint(); |
92 | < | mpiEventLoop(); |
89 | > | set_interface_stamps(stamps, simParams); |
90 | > | mpiEventInit(); |
91 | > | MPIcheckPoint(); |
92 | > | mpiEventLoop(); |
93 | } | |
94 | < | |
94 | > | |
95 | #endif | |
96 | – | |
97 | – | } |
98 | – | |
99 | – | SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
96 | ||
97 | + | } |
98 | + | |
99 | + | SimInfo* SimCreator::createSim(const std::string & mdFileName, |
100 | + | bool loadInitCoords) { |
101 | + | |
102 | MakeStamps * stamps = new MakeStamps(); | |
103 | < | |
103 | > | |
104 | Globals * simParams = new Globals(); | |
105 | < | |
105 | > | |
106 | //parse meta-data file | |
107 | parseFile(mdFileName, stamps, simParams); | |
108 | < | |
108 | > | |
109 | //create the force field | |
110 | < | ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
111 | < | simParams->getForceField()); |
110 | > | ForceField * ff = ForceFieldFactory::getInstance() |
111 | > | ->createForceField(simParams->getForceField()); |
112 | ||
113 | if (ff == NULL) { | |
114 | < | sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
115 | < | simParams->getForceField()); |
116 | < | painCave.isFatal = 1; |
117 | < | simError(); |
114 | > | sprintf(painCave.errMsg, |
115 | > | "ForceField Factory can not create %s force field\n", |
116 | > | simParams->getForceField()); |
117 | > | painCave.isFatal = 1; |
118 | > | simError(); |
119 | } | |
120 | < | |
120 | > | |
121 | > | if (simParams->haveForceFieldFileName()) { |
122 | > | ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
123 | > | } |
124 | > | |
125 | std::string forcefieldFileName; | |
126 | forcefieldFileName = ff->getForceFieldFileName(); | |
127 | < | |
127 | > | |
128 | if (simParams->haveForceFieldVariant()) { | |
129 | < | //If the force field has variant, the variant force field name will be |
130 | < | //Base.variant.frc. For exampel EAM.u6.frc |
131 | < | |
132 | < | std::string variant = simParams->getForceFieldVariant(); |
133 | < | |
134 | < | std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
135 | < | variant = "." + variant; |
136 | < | if (pos != std::string::npos) { |
137 | < | forcefieldFileName.insert(pos, variant); |
138 | < | } else { |
139 | < | //If the default force field file name does not containt .frc suffix, just append the .variant |
140 | < | forcefieldFileName.append(variant); |
141 | < | } |
129 | > | //If the force field has variant, the variant force field name will be |
130 | > | //Base.variant.frc. For exampel EAM.u6.frc |
131 | > | |
132 | > | std::string variant = simParams->getForceFieldVariant(); |
133 | > | |
134 | > | std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
135 | > | variant = "." + variant; |
136 | > | if (pos != std::string::npos) { |
137 | > | forcefieldFileName.insert(pos, variant); |
138 | > | } else { |
139 | > | //If the default force field file name does not containt .frc suffix, just append the .variant |
140 | > | forcefieldFileName.append(variant); |
141 | > | } |
142 | } | |
143 | ||
144 | ff->parse(forcefieldFileName); | |
# | Line 140 | Line 146 | SimInfo* SimCreator::createSim(const std::string & md | |
146 | //extract the molecule stamps | |
147 | std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; | |
148 | compList(stamps, simParams, moleculeStampPairs); | |
149 | < | |
149 | > | |
150 | //create SimInfo | |
151 | < | SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
152 | < | |
151 | > | SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
152 | > | |
153 | //gather parameters (SimCreator only retrieves part of the parameters) | |
154 | gatherParameters(info, mdFileName); | |
155 | < | |
155 | > | |
156 | //divide the molecules and determine the global index of molecules | |
157 | #ifdef IS_MPI | |
158 | divideMolecules(info); | |
159 | #endif | |
160 | < | |
160 | > | |
161 | //create the molecules | |
162 | createMolecules(info); | |
163 | < | |
164 | < | |
163 | > | |
164 | > | |
165 | //allocate memory for DataStorage(circular reference, need to break it) | |
166 | info->setSnapshotManager(new SimSnapshotManager(info)); | |
167 | ||
# | Line 163 | Line 169 | SimInfo* SimCreator::createSim(const std::string & md | |
169 | //global index will never change again). Local indices of atoms and rigidbodies are already set by | |
170 | //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. | |
171 | setGlobalIndex(info); | |
172 | < | |
172 | > | |
173 | //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point | |
174 | //atoms don't have the global index yet (their global index are all initialized to -1). | |
175 | //Therefore we have to call addExcludePairs explicitly here. A way to work around is that | |
# | Line 171 | Line 177 | SimInfo* SimCreator::createSim(const std::string & md | |
177 | SimInfo::MoleculeIterator mi; | |
178 | Molecule* mol; | |
179 | for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { | |
180 | < | info->addExcludePairs(mol); |
180 | > | info->addExcludePairs(mol); |
181 | } | |
182 | ||
177 | – | |
178 | – | //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
179 | – | //eta, chi for NPT integrator) |
183 | if (loadInitCoords) | |
184 | < | loadCoordinates(info); |
184 | > | loadCoordinates(info); |
185 | ||
186 | return info; | |
187 | < | } |
188 | < | |
189 | < | void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
190 | < | |
188 | < | //setup seed for random number generator |
189 | < | int seedValue; |
190 | < | Globals * simParams = info->getSimParams(); |
191 | < | |
192 | < | if (simParams->haveSeed()) { |
193 | < | seedValue = simParams->getSeed(); |
194 | < | |
195 | < | if (seedValue < 100000000 ) { |
196 | < | sprintf(painCave.errMsg, |
197 | < | "Seed for sprng library should contain at least 9 digits\n" |
198 | < | "OOPSE will generate a seed for user\n"); |
199 | < | |
200 | < | painCave.isFatal = 0; |
201 | < | simError(); |
202 | < | |
203 | < | //using seed generated by system instead of invalid seed set by user |
204 | < | |
205 | < | #ifndef IS_MPI |
206 | < | |
207 | < | seedValue = make_sprng_seed(); |
208 | < | |
209 | < | #else |
210 | < | |
211 | < | if (worldRank == 0) { |
212 | < | seedValue = make_sprng_seed(); |
213 | < | } |
214 | < | |
215 | < | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
216 | < | |
217 | < | #endif |
218 | < | |
219 | < | } //end if (seedValue /1000000000 == 0) |
220 | < | } else { |
221 | < | |
222 | < | #ifndef IS_MPI |
223 | < | |
224 | < | seedValue = make_sprng_seed(); |
225 | < | |
226 | < | #else |
227 | < | |
228 | < | if (worldRank == 0) { |
229 | < | seedValue = make_sprng_seed(); |
230 | < | } |
231 | < | |
232 | < | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
233 | < | |
234 | < | #endif |
235 | < | |
236 | < | } //end of simParams->haveSeed() |
237 | < | |
238 | < | info->setSeed(seedValue); |
239 | < | |
240 | < | |
187 | > | } |
188 | > | |
189 | > | void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
190 | > | |
191 | //figure out the ouput file names | |
192 | std::string prefix; | |
193 | < | |
193 | > | |
194 | #ifdef IS_MPI | |
195 | < | |
195 | > | |
196 | if (worldRank == 0) { | |
197 | #endif // is_mpi | |
198 | < | |
199 | < | if (simParams->haveFinalConfig()) { |
200 | < | prefix = getPrefix(simParams->getFinalConfig()); |
201 | < | } else { |
202 | < | prefix = getPrefix(mdfile); |
203 | < | } |
204 | < | |
205 | < | info->setFinalConfigFileName(prefix + ".eor"); |
206 | < | info->setDumpFileName(prefix + ".dump"); |
207 | < | info->setStatFileName(prefix + ".stat"); |
208 | < | |
198 | > | Globals * simParams = info->getSimParams(); |
199 | > | if (simParams->haveFinalConfig()) { |
200 | > | prefix = getPrefix(simParams->getFinalConfig()); |
201 | > | } else { |
202 | > | prefix = getPrefix(mdfile); |
203 | > | } |
204 | > | |
205 | > | info->setFinalConfigFileName(prefix + ".eor"); |
206 | > | info->setDumpFileName(prefix + ".dump"); |
207 | > | info->setStatFileName(prefix + ".stat"); |
208 | > | info->setRestFileName(prefix + ".zang"); |
209 | > | |
210 | #ifdef IS_MPI | |
211 | < | |
211 | > | |
212 | } | |
213 | < | |
213 | > | |
214 | #endif | |
215 | < | |
216 | < | } |
217 | < | |
215 | > | |
216 | > | } |
217 | > | |
218 | #ifdef IS_MPI | |
219 | < | void SimCreator::divideMolecules(SimInfo *info) { |
219 | > | void SimCreator::divideMolecules(SimInfo *info) { |
220 | double numerator; | |
221 | double denominator; | |
222 | double precast; | |
# | Line 283 | Line 234 | void SimCreator::divideMolecules(SimInfo *info) { | |
234 | int which_proc; | |
235 | int nProcessors; | |
236 | std::vector<int> atomsPerProc; | |
286 | – | randomSPRNG myRandom(info->getSeed()); |
237 | int nGlobalMols = info->getNGlobalMolecules(); | |
238 | std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: | |
239 | ||
240 | MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); | |
241 | < | |
241 | > | |
242 | if (nProcessors > nGlobalMols) { | |
243 | < | sprintf(painCave.errMsg, |
244 | < | "nProcessors (%d) > nMol (%d)\n" |
245 | < | "\tThe number of processors is larger than\n" |
246 | < | "\tthe number of molecules. This will not result in a \n" |
247 | < | "\tusable division of atoms for force decomposition.\n" |
248 | < | "\tEither try a smaller number of processors, or run the\n" |
249 | < | "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
250 | < | |
251 | < | painCave.isFatal = 1; |
252 | < | simError(); |
243 | > | sprintf(painCave.errMsg, |
244 | > | "nProcessors (%d) > nMol (%d)\n" |
245 | > | "\tThe number of processors is larger than\n" |
246 | > | "\tthe number of molecules. This will not result in a \n" |
247 | > | "\tusable division of atoms for force decomposition.\n" |
248 | > | "\tEither try a smaller number of processors, or run the\n" |
249 | > | "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
250 | > | |
251 | > | painCave.isFatal = 1; |
252 | > | simError(); |
253 | } | |
254 | < | |
254 | > | |
255 | > | int seedValue; |
256 | > | Globals * simParams = info->getSimParams(); |
257 | > | SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
258 | > | if (simParams->haveSeed()) { |
259 | > | seedValue = simParams->getSeed(); |
260 | > | myRandom = new SeqRandNumGen(seedValue); |
261 | > | }else { |
262 | > | myRandom = new SeqRandNumGen(); |
263 | > | } |
264 | > | |
265 | > | |
266 | a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); | |
267 | < | |
267 | > | |
268 | //initialize atomsPerProc | |
269 | atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); | |
270 | < | |
270 | > | |
271 | if (worldRank == 0) { | |
272 | < | numerator = info->getNGlobalAtoms(); |
273 | < | denominator = nProcessors; |
274 | < | precast = numerator / denominator; |
275 | < | nTarget = (int)(precast + 0.5); |
276 | < | |
277 | < | for(i = 0; i < nGlobalMols; i++) { |
278 | < | done = 0; |
279 | < | loops = 0; |
280 | < | |
281 | < | while (!done) { |
282 | < | loops++; |
283 | < | |
284 | < | // Pick a processor at random |
285 | < | |
286 | < | which_proc = (int) (myRandom.getRandom() * nProcessors); |
287 | < | |
288 | < | //get the molecule stamp first |
289 | < | int stampId = info->getMoleculeStampId(i); |
290 | < | MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
291 | < | |
292 | < | // How many atoms does this processor have so far? |
293 | < | old_atoms = atomsPerProc[which_proc]; |
294 | < | add_atoms = moleculeStamp->getNAtoms(); |
295 | < | new_atoms = old_atoms + add_atoms; |
296 | < | |
297 | < | // If we've been through this loop too many times, we need |
298 | < | // to just give up and assign the molecule to this processor |
299 | < | // and be done with it. |
300 | < | |
301 | < | if (loops > 100) { |
302 | < | sprintf(painCave.errMsg, |
303 | < | "I've tried 100 times to assign molecule %d to a " |
304 | < | " processor, but can't find a good spot.\n" |
305 | < | "I'm assigning it at random to processor %d.\n", |
306 | < | i, which_proc); |
307 | < | |
308 | < | painCave.isFatal = 0; |
309 | < | simError(); |
310 | < | |
311 | < | molToProcMap[i] = which_proc; |
312 | < | atomsPerProc[which_proc] += add_atoms; |
313 | < | |
314 | < | done = 1; |
315 | < | continue; |
316 | < | } |
317 | < | |
318 | < | // If we can add this molecule to this processor without sending |
319 | < | // it above nTarget, then go ahead and do it: |
320 | < | |
321 | < | if (new_atoms <= nTarget) { |
322 | < | molToProcMap[i] = which_proc; |
323 | < | atomsPerProc[which_proc] += add_atoms; |
324 | < | |
325 | < | done = 1; |
326 | < | continue; |
327 | < | } |
328 | < | |
329 | < | // The only situation left is when new_atoms > nTarget. We |
330 | < | // want to accept this with some probability that dies off the |
331 | < | // farther we are from nTarget |
332 | < | |
333 | < | // roughly: x = new_atoms - nTarget |
334 | < | // Pacc(x) = exp(- a * x) |
335 | < | // where a = penalty / (average atoms per molecule) |
336 | < | |
337 | < | x = (double)(new_atoms - nTarget); |
338 | < | y = myRandom.getRandom(); |
339 | < | |
340 | < | if (y < exp(- a * x)) { |
341 | < | molToProcMap[i] = which_proc; |
342 | < | atomsPerProc[which_proc] += add_atoms; |
343 | < | |
344 | < | done = 1; |
345 | < | continue; |
346 | < | } else { |
347 | < | continue; |
348 | < | } |
349 | < | } |
350 | < | } |
351 | < | |
352 | < | // Spray out this nonsense to all other processors: |
353 | < | |
354 | < | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
355 | < | } else { |
356 | < | |
357 | < | // Listen to your marching orders from processor 0: |
358 | < | |
359 | < | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
272 | > | numerator = info->getNGlobalAtoms(); |
273 | > | denominator = nProcessors; |
274 | > | precast = numerator / denominator; |
275 | > | nTarget = (int)(precast + 0.5); |
276 | > | |
277 | > | for(i = 0; i < nGlobalMols; i++) { |
278 | > | done = 0; |
279 | > | loops = 0; |
280 | > | |
281 | > | while (!done) { |
282 | > | loops++; |
283 | > | |
284 | > | // Pick a processor at random |
285 | > | |
286 | > | which_proc = (int) (myRandom->rand() * nProcessors); |
287 | > | |
288 | > | //get the molecule stamp first |
289 | > | int stampId = info->getMoleculeStampId(i); |
290 | > | MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
291 | > | |
292 | > | // How many atoms does this processor have so far? |
293 | > | old_atoms = atomsPerProc[which_proc]; |
294 | > | add_atoms = moleculeStamp->getNAtoms(); |
295 | > | new_atoms = old_atoms + add_atoms; |
296 | > | |
297 | > | // If we've been through this loop too many times, we need |
298 | > | // to just give up and assign the molecule to this processor |
299 | > | // and be done with it. |
300 | > | |
301 | > | if (loops > 100) { |
302 | > | sprintf(painCave.errMsg, |
303 | > | "I've tried 100 times to assign molecule %d to a " |
304 | > | " processor, but can't find a good spot.\n" |
305 | > | "I'm assigning it at random to processor %d.\n", |
306 | > | i, which_proc); |
307 | > | |
308 | > | painCave.isFatal = 0; |
309 | > | simError(); |
310 | > | |
311 | > | molToProcMap[i] = which_proc; |
312 | > | atomsPerProc[which_proc] += add_atoms; |
313 | > | |
314 | > | done = 1; |
315 | > | continue; |
316 | > | } |
317 | > | |
318 | > | // If we can add this molecule to this processor without sending |
319 | > | // it above nTarget, then go ahead and do it: |
320 | > | |
321 | > | if (new_atoms <= nTarget) { |
322 | > | molToProcMap[i] = which_proc; |
323 | > | atomsPerProc[which_proc] += add_atoms; |
324 | > | |
325 | > | done = 1; |
326 | > | continue; |
327 | > | } |
328 | > | |
329 | > | // The only situation left is when new_atoms > nTarget. We |
330 | > | // want to accept this with some probability that dies off the |
331 | > | // farther we are from nTarget |
332 | > | |
333 | > | // roughly: x = new_atoms - nTarget |
334 | > | // Pacc(x) = exp(- a * x) |
335 | > | // where a = penalty / (average atoms per molecule) |
336 | > | |
337 | > | x = (double)(new_atoms - nTarget); |
338 | > | y = myRandom->rand(); |
339 | > | |
340 | > | if (y < exp(- a * x)) { |
341 | > | molToProcMap[i] = which_proc; |
342 | > | atomsPerProc[which_proc] += add_atoms; |
343 | > | |
344 | > | done = 1; |
345 | > | continue; |
346 | > | } else { |
347 | > | continue; |
348 | > | } |
349 | > | } |
350 | > | } |
351 | > | |
352 | > | delete myRandom; |
353 | > | |
354 | > | // Spray out this nonsense to all other processors: |
355 | > | |
356 | > | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
357 | > | } else { |
358 | > | |
359 | > | // Listen to your marching orders from processor 0: |
360 | > | |
361 | > | MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
362 | } | |
363 | < | |
363 | > | |
364 | info->setMolToProcMap(molToProcMap); | |
365 | sprintf(checkPointMsg, | |
366 | "Successfully divided the molecules among the processors.\n"); | |
367 | MPIcheckPoint(); | |
368 | < | } |
369 | < | |
368 | > | } |
369 | > | |
370 | #endif | |
371 | < | |
372 | < | void SimCreator::createMolecules(SimInfo *info) { |
371 | > | |
372 | > | void SimCreator::createMolecules(SimInfo *info) { |
373 | MoleculeCreator molCreator; | |
374 | int stampId; | |
375 | < | |
375 | > | |
376 | for(int i = 0; i < info->getNGlobalMolecules(); i++) { | |
377 | < | |
377 | > | |
378 | #ifdef IS_MPI | |
379 | < | |
380 | < | if (info->getMolToProc(i) == worldRank) { |
379 | > | |
380 | > | if (info->getMolToProc(i) == worldRank) { |
381 | #endif | |
382 | < | |
383 | < | stampId = info->getMoleculeStampId(i); |
384 | < | Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
385 | < | stampId, i, info->getLocalIndexManager()); |
386 | < | |
387 | < | info->addMolecule(mol); |
388 | < | |
382 | > | |
383 | > | stampId = info->getMoleculeStampId(i); |
384 | > | Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
385 | > | stampId, i, info->getLocalIndexManager()); |
386 | > | |
387 | > | info->addMolecule(mol); |
388 | > | |
389 | #ifdef IS_MPI | |
390 | < | |
391 | < | } |
392 | < | |
390 | > | |
391 | > | } |
392 | > | |
393 | #endif | |
394 | < | |
394 | > | |
395 | } //end for(int i=0) | |
396 | < | } |
397 | < | |
398 | < | void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
399 | < | std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
396 | > | } |
397 | > | |
398 | > | void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
399 | > | std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
400 | int i; | |
401 | char * id; | |
402 | MoleculeStamp * currentStamp; | |
403 | Component** the_components = simParams->getComponents(); | |
404 | int n_components = simParams->getNComponents(); | |
405 | < | |
405 | > | |
406 | if (!simParams->haveNMol()) { | |
407 | < | // we don't have the total number of molecules, so we assume it is |
408 | < | // given in each component |
407 | > | // we don't have the total number of molecules, so we assume it is |
408 | > | // given in each component |
409 | > | |
410 | > | for(i = 0; i < n_components; i++) { |
411 | > | if (!the_components[i]->haveNMol()) { |
412 | > | // we have a problem |
413 | > | sprintf(painCave.errMsg, |
414 | > | "SimCreator Error. No global NMol or component NMol given.\n" |
415 | > | "\tCannot calculate the number of atoms.\n"); |
416 | > | |
417 | > | painCave.isFatal = 1; |
418 | > | simError(); |
419 | > | } |
420 | > | |
421 | > | id = the_components[i]->getType(); |
422 | ||
423 | < | for(i = 0; i < n_components; i++) { |
424 | < | if (!the_components[i]->haveNMol()) { |
425 | < | // we have a problem |
426 | < | sprintf(painCave.errMsg, |
427 | < | "SimCreator Error. No global NMol or component NMol given.\n" |
428 | < | "\tCannot calculate the number of atoms.\n"); |
429 | < | |
430 | < | painCave.isFatal = 1; |
431 | < | simError(); |
432 | < | } |
433 | < | |
434 | < | id = the_components[i]->getType(); |
435 | < | currentStamp = (stamps->extractMolStamp(id))->getStamp(); |
460 | < | |
461 | < | if (currentStamp == NULL) { |
462 | < | sprintf(painCave.errMsg, |
463 | < | "SimCreator error: Component \"%s\" was not found in the " |
464 | < | "list of declared molecules\n", id); |
465 | < | |
466 | < | painCave.isFatal = 1; |
467 | < | simError(); |
468 | < | } |
469 | < | |
470 | < | moleculeStampPairs.push_back( |
471 | < | std::make_pair(currentStamp, the_components[i]->getNMol())); |
472 | < | } //end for (i = 0; i < n_components; i++) |
423 | > | currentStamp = stamps->getMolStamp(id); |
424 | > | if (currentStamp == NULL) { |
425 | > | sprintf(painCave.errMsg, |
426 | > | "SimCreator error: Component \"%s\" was not found in the " |
427 | > | "list of declared molecules\n", id); |
428 | > | |
429 | > | painCave.isFatal = 1; |
430 | > | simError(); |
431 | > | } |
432 | > | |
433 | > | moleculeStampPairs.push_back( |
434 | > | std::make_pair(currentStamp, the_components[i]->getNMol())); |
435 | > | } //end for (i = 0; i < n_components; i++) |
436 | } else { | |
437 | < | sprintf(painCave.errMsg, "SimSetup error.\n" |
438 | < | "\tSorry, the ability to specify total" |
439 | < | " nMols and then give molfractions in the components\n" |
440 | < | "\tis not currently supported." |
441 | < | " Please give nMol in the components.\n"); |
442 | < | |
443 | < | painCave.isFatal = 1; |
444 | < | simError(); |
437 | > | sprintf(painCave.errMsg, "SimSetup error.\n" |
438 | > | "\tSorry, the ability to specify total" |
439 | > | " nMols and then give molfractions in the components\n" |
440 | > | "\tis not currently supported." |
441 | > | " Please give nMol in the components.\n"); |
442 | > | |
443 | > | painCave.isFatal = 1; |
444 | > | simError(); |
445 | } | |
446 | < | |
446 | > | |
447 | #ifdef IS_MPI | |
448 | < | |
448 | > | |
449 | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); | |
450 | MPIcheckPoint(); | |
451 | < | |
451 | > | |
452 | #endif // is_mpi | |
453 | < | |
454 | < | } |
455 | < | |
456 | < | void SimCreator::setGlobalIndex(SimInfo *info) { |
453 | > | |
454 | > | } |
455 | > | |
456 | > | void SimCreator::setGlobalIndex(SimInfo *info) { |
457 | SimInfo::MoleculeIterator mi; | |
458 | Molecule::AtomIterator ai; | |
459 | Molecule::RigidBodyIterator ri; | |
# | Line 505 | Line 468 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
468 | int nGlobalAtoms = info->getNGlobalAtoms(); | |
469 | ||
470 | #ifndef IS_MPI | |
471 | < | |
471 | > | |
472 | beginAtomIndex = 0; | |
473 | beginRigidBodyIndex = 0; | |
474 | beginCutoffGroupIndex = 0; | |
475 | < | |
475 | > | |
476 | #else | |
477 | < | |
477 | > | |
478 | int nproc; | |
479 | int myNode; | |
480 | < | |
480 | > | |
481 | myNode = worldRank; | |
482 | MPI_Comm_size(MPI_COMM_WORLD, &nproc); | |
483 | < | |
483 | > | |
484 | std::vector < int > tmpAtomsInProc(nproc, 0); | |
485 | std::vector < int > tmpRigidBodiesInProc(nproc, 0); | |
486 | std::vector < int > tmpCutoffGroupsInProc(nproc, 0); | |
487 | std::vector < int > NumAtomsInProc(nproc, 0); | |
488 | std::vector < int > NumRigidBodiesInProc(nproc, 0); | |
489 | std::vector < int > NumCutoffGroupsInProc(nproc, 0); | |
490 | < | |
490 | > | |
491 | tmpAtomsInProc[myNode] = info->getNAtoms(); | |
492 | tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); | |
493 | tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); | |
494 | < | |
494 | > | |
495 | //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups | |
496 | MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, | |
497 | MPI_SUM, MPI_COMM_WORLD); | |
# | Line 536 | Line 499 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
499 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
500 | MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, | |
501 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
502 | < | |
502 | > | |
503 | beginAtomIndex = 0; | |
504 | beginRigidBodyIndex = 0; | |
505 | beginCutoffGroupIndex = 0; | |
506 | < | |
506 | > | |
507 | for(int i = 0; i < myNode; i++) { | |
508 | < | beginAtomIndex += NumAtomsInProc[i]; |
509 | < | beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
510 | < | beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
508 | > | beginAtomIndex += NumAtomsInProc[i]; |
509 | > | beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
510 | > | beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
511 | } | |
512 | < | |
512 | > | |
513 | #endif | |
514 | < | |
514 | > | |
515 | > | //rigidbody's index begins right after atom's |
516 | > | beginRigidBodyIndex += info->getNGlobalAtoms(); |
517 | > | |
518 | for(mol = info->beginMolecule(mi); mol != NULL; | |
519 | mol = info->nextMolecule(mi)) { | |
520 | < | |
521 | < | //local index(index in DataStorge) of atom is important |
522 | < | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
523 | < | atom->setGlobalIndex(beginAtomIndex++); |
524 | < | } |
525 | < | |
526 | < | for(rb = mol->beginRigidBody(ri); rb != NULL; |
527 | < | rb = mol->nextRigidBody(ri)) { |
528 | < | rb->setGlobalIndex(beginRigidBodyIndex++); |
529 | < | } |
530 | < | |
531 | < | //local index of cutoff group is trivial, it only depends on the order of travesing |
532 | < | for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
533 | < | cg = mol->nextCutoffGroup(ci)) { |
534 | < | cg->setGlobalIndex(beginCutoffGroupIndex++); |
535 | < | } |
520 | > | |
521 | > | //local index(index in DataStorge) of atom is important |
522 | > | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
523 | > | atom->setGlobalIndex(beginAtomIndex++); |
524 | > | } |
525 | > | |
526 | > | for(rb = mol->beginRigidBody(ri); rb != NULL; |
527 | > | rb = mol->nextRigidBody(ri)) { |
528 | > | rb->setGlobalIndex(beginRigidBodyIndex++); |
529 | > | } |
530 | > | |
531 | > | //local index of cutoff group is trivial, it only depends on the order of travesing |
532 | > | for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
533 | > | cg = mol->nextCutoffGroup(ci)) { |
534 | > | cg->setGlobalIndex(beginCutoffGroupIndex++); |
535 | > | } |
536 | } | |
537 | < | |
537 | > | |
538 | //fill globalGroupMembership | |
539 | std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); | |
540 | for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { | |
541 | < | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
542 | < | |
543 | < | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
544 | < | globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
545 | < | } |
546 | < | |
547 | < | } |
541 | > | for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
542 | > | |
543 | > | for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
544 | > | globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
545 | > | } |
546 | > | |
547 | > | } |
548 | } | |
549 | < | |
549 | > | |
550 | #ifdef IS_MPI | |
551 | // Since the globalGroupMembership has been zero filled and we've only | |
552 | // poked values into the atoms we know, we can do an Allreduce | |
# | Line 590 | Line 556 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
556 | std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); | |
557 | MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, | |
558 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
559 | < | info->setGlobalGroupMembership(tmpGroupMembership); |
559 | > | info->setGlobalGroupMembership(tmpGroupMembership); |
560 | #else | |
561 | info->setGlobalGroupMembership(globalGroupMembership); | |
562 | #endif | |
563 | < | |
563 | > | |
564 | //fill molMembership | |
565 | std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); | |
566 | ||
567 | for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { | |
568 | < | |
569 | < | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
570 | < | globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
571 | < | } |
568 | > | |
569 | > | for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
570 | > | globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
571 | > | } |
572 | } | |
573 | < | |
573 | > | |
574 | #ifdef IS_MPI | |
575 | std::vector<int> tmpMolMembership(nGlobalAtoms, 0); | |
576 | < | |
576 | > | |
577 | MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, | |
578 | MPI_INT, MPI_SUM, MPI_COMM_WORLD); | |
579 | ||
# | Line 615 | Line 581 | void SimCreator::setGlobalIndex(SimInfo *info) { | |
581 | #else | |
582 | info->setGlobalMolMembership(globalMolMembership); | |
583 | #endif | |
584 | < | |
585 | < | } |
586 | < | |
587 | < | void SimCreator::loadCoordinates(SimInfo* info) { |
584 | > | |
585 | > | } |
586 | > | |
587 | > | void SimCreator::loadCoordinates(SimInfo* info) { |
588 | Globals* simParams; | |
589 | simParams = info->getSimParams(); | |
590 | ||
591 | if (!simParams->haveInitialConfig()) { | |
592 | < | sprintf(painCave.errMsg, |
593 | < | "Cannot intialize a simulation without an initial configuration file.\n"); |
594 | < | painCave.isFatal = 1;; |
595 | < | simError(); |
592 | > | sprintf(painCave.errMsg, |
593 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
594 | > | painCave.isFatal = 1;; |
595 | > | simError(); |
596 | } | |
597 | < | |
597 | > | |
598 | DumpReader reader(info, simParams->getInitialConfig()); | |
599 | int nframes = reader.getNFrames(); | |
600 | < | |
600 | > | |
601 | if (nframes > 0) { | |
602 | < | reader.readFrame(nframes - 1); |
602 | > | reader.readFrame(nframes - 1); |
603 | } else { | |
604 | < | //invalid initial coordinate file |
605 | < | sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
606 | < | simParams->getInitialConfig()); |
607 | < | painCave.isFatal = 1; |
608 | < | simError(); |
604 | > | //invalid initial coordinate file |
605 | > | sprintf(painCave.errMsg, |
606 | > | "Initial configuration file %s should at least contain one frame\n", |
607 | > | simParams->getInitialConfig()); |
608 | > | painCave.isFatal = 1; |
609 | > | simError(); |
610 | } | |
611 | < | |
611 | > | |
612 | //copy the current snapshot to previous snapshot | |
613 | info->getSnapshotManager()->advance(); | |
614 | < | } |
615 | < | |
614 | > | } |
615 | > | |
616 | } //end namespace oopse | |
617 | ||
618 |
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